Abstract

Protein nanobodies have been used successfully as surrogates for unstable G-proteins in order to crystallize G-protein-coupled receptors (GPCRs) in their active states. We used molecular dynamics (MD) simulations, including meta-dynamics enhanced sampling, to investigate the similarities and differences between GPCR-agonist ternary complexes with the alpha-subunits of the appropriate G-proteins and those with the protein nanobodies (intracellular binding partners, IBPs) used for crystallization. In two of the three receptors considered, the agonist-binding mode differs significantly between the two alternative ternary complexes. The ternary-complex model of GPCR activation entails enhancement of ligand binding by bound IBPs: Our results show that IBP-specific changes can alter the agonist binding modes and thus also the criteria for designing GPCR agonists.